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The Cell – Comprehensive Notes

What is a Cell?

  • Definition: The cell is the smallest living structure that serves as the basic unit of structure and function for an organism.
  • Composition: Cells are composed of atoms and molecules.
  • Diversity: Cells have widely varying structures based on their functions.
  • Primary components to know:
    • Plasma membrane: Outer limiting barrier between inside and outside of the cell.
    • Nucleus: Largest structure in a cell; contains genetic material (DNA).
    • Cytoplasm: All cellular components between the nucleus and the plasma membrane; consists of cytosol (fluid) and organelles; includes inclusions (clusters of a single type of molecule, e.g., pigments).

General Cell Features and Principal Components

  • Common features across cells: Plasma membrane, nucleus, cytoplasm (cytosol + organelles + inclusions).
  • Cytoplasm: Region between nucleus and plasma membrane including:
    • Cytosol: intracellular fluid.
    • Organelles: membrane-bound or non-membrane-bound structures with specialized functions.
    • Inclusions: aggregates of a single type of molecule (e.g., pigments).
  • Nucleus: Includes genetic material and control cellular activities; houses nucleolus (ribosome production) and is enclosed by the nuclear envelope.

Cellular Architecture – Key Organelles (Figure references)

  • Non-membrane-bound organelles:
    • Ribosomes: free ribosomes and bound ribosomes.
    • Centrosome
    • Proteasomes
    • Cytoskeleton
    • Cytosol (intracellular fluid) and interstitial fluid
    • Nucleoplasm, Nucleolus, Nuclear envelope, Nucleus
  • Membrane-bound organelles:
    • Rough endoplasmic reticulum (RER)
    • Smooth endoplasmic reticulum (SER)
    • Golgi apparatus
    • Lysosome
    • Peroxisome
    • Vesicles
    • Inclusions
    • Mitochondrion
  • Cytoplasmic context: Cytoplasm, including cytosol and organelles, and plasma membrane forms the cell boundary.
  • Modifications of the plasma membrane: Microvilli, Cilia, Flagellum.

Plasma Membrane – Structure and Components

  • Structure: Fluid-mosaic model; lipid bilayer with embedded proteins.
  • Lipid bilayer: Phospholipids arranged with hydrophilic (polar) heads facing cytoplasm and interstitial fluid, and hydrophobic tails facing each other.
  • Cholesterol: Strengthens the membrane.
  • Membrane proteins: Integral (span the membrane) or peripheral (attached to membrane surface).
  • Functions of membrane proteins:
    • Transporters (channels and carriers)
    • Receptors
    • Identity markers
    • Enzymes
    • Anchoring sites
    • Cell-adhesion proteins
  • Glycocalyx: Carbohydrate-rich coating associated with the plasma membrane that includes glycoproteins and glycolipids.

Plasma Membrane – Functions

  • Physical barrier: Flexible boundary that protects cellular contents and supports cell structure.
  • Selectively permeable boundary: Regulates entry and exit of ions, nutrients, and wastes.
  • Establishes and maintains electrochemical gradients across the membrane.
  • Communication: Contains receptors that recognize and respond to molecular signals.

Membrane Transport – Overview

  • Transport across the plasma membrane can be passive (no energy) or active (energy requiring).
  • Passive transport options:
    • Diffusion: Movement of a solute down its concentration gradient.
    • Simple diffusion: No transport protein required; small nonpolar molecules move directly through the lipid bilayer.
    • Facilitated diffusion: Requires transport proteins; can be channel-mediated or carrier-mediated.
    • Osmosis: Movement of water across the membrane.
  • Active transport options:
    • Requires energy (usually ATP) to move substances against their concentration gradient or to form vesicles (endocytosis/exocytosis).
    • Primary active transport: Energy from ATP hydrolysis; pumps move substances uphill.
    • Secondary active transport: Energy from movement of another substance down its gradient (e.g., Na+ gradient drives transport of another solute).
    • Vesicular transport: Exocytosis and Endocytosis (including phagocytosis, pinocytosis, receptor-mediated endocytosis).

Diffusion, Facilitated Diffusion, and Osmosis – Details

  • Simple diffusion: Small, nonpolar solutes move down their concentration gradients without transport proteins. Examples: O2, CO2.
  • Facilitated diffusion: Polar or charged solutes require transport proteins.
    • Channel-mediated: Ions move through water-filled channels (e.g., Na+ channels).
    • Carrier-mediated: Carrier proteins change shape to transport polar molecules (e.g., glucose).
  • Osmosis: Water movement across a semipermeable membrane, often via aquaporins; water moves toward higher solute concentration.
  • Key concept: Osmolarity and tonicity (isotonic, hypotonic, hypertonic) determine water movement and cell volume.

Example Figures and Concepts

  • Simple diffusion (Fig. 4.9): Oxygen and carbon dioxide diffuse across cytosol.
  • Facilitated diffusion (Fig. 4.10): Glucose via carrier, Na+ through channels; carrier proteins change shape to transport small polar molecules.
  • Osmosis (Fig. 4.11): Aquaporin-facilitated water movement; non-permeable to most solutes (e.g., ions, glucose).
  • Erythrocyte in isotonic/hypotonic/hypertonic solutions (Fig. 4.13): Isotonic: interstitial fluid equals cytosol; Hypotonic: higher water concentration outside; Hypertonic: lower water concentration outside; outcomes include crenation or lysis depending on tonicity.

Active Transport and Vesicular Transport

  • Primary active transport: Direct use of ATP; e.g., Ca2+ pump (Fig. 4.14) uses ATP to move Ca2+ against its gradient.
    • Reaction: ATP → ADP + Pi; energy drives pump conformational changes.
  • Secondary active transport: Uses energy from a primary transport process (e.g., Na+ gradient) to move another solute.
    • Examples: Symport (molecules moved in same direction) and antiport (molecules moved in opposite directions) (Fig. 4.16).
  • Vesicular transport: Movement of substances via vesicles; requires vesicle formation.
    • Exocytosis: Vesicle fuses with plasma membrane to release contents outside the cell.
    • Endocytosis: Material brought into the cell via vesicle formation.
    • Phagocytosis: Cellular “eating” (particle uptake, e.g., phagocytes engulfing bacteria).
    • Pinocytosis: Cellular “drinking” (fluid uptake via vesicles).
    • Receptor-mediated endocytosis: Ligands bind receptors, are internalized in clathrin-coated vesicles.
  • Exocytosis and endocytosis steps (Fig. 4.17): Vesicle approach, docking, fusion, and release of contents; vesicle membrane components integrate into the plasma membrane.
  • Endocytosis overview (Fig. 4.18-4.19): Three forms—phagocytosis, pinocytosis, receptor-mediated endocytosis; clathrin-coated pits and vesicles involved.

Endomembrane System

  • Includes internal membranes that work together to synthesize, modify, and ship proteins and lipids:
    • Rough ER: Synthesizes and modifies proteins; produces transport vesicles; ribosomes attach to the surface.
    • Smooth ER: Lipid synthesis; carbohydrate metabolism; detoxification; forms transport vesicles.
    • Golgi apparatus: Modifies, packages, and sorts proteins; forms proteoglycans; vesicle formation for transport to plasma membrane or lysosomes.
    • Lysosome: Digestive enzymes for breakdown of molecules within vesicles; part of intracellular digestion.
    • Peroxisome: Detoxification and lipid metabolism (mentioned in ER context).
  • Transport through the endomembrane system: ER → Golgi → secretory/transport vesicles → plasma membrane or lysosomes (Fig. 4.23a/b).
  • Proteins from Rough ER are processed through Golgi (glycosylation, sorting) and directed to their destinations (exocytosis, insertion into plasma membrane, lysosomal enzymes).

Golgi Apparatus and Endomembrane System – Detailed Functions

  • Golgi apparatus structure: Series of cisternae (cis-face and trans-face).
  • Functions:
    • Synthesis of proteoglycans and synthesis/modification of proteins produced by Rough ER.
    • Packaging into secretory vesicles; formation of lysosomal enzymes.
    • Vesicle formation for delivering membrane components and exocytosis.
  • Endomembrane system diagram shows the flow from Rough ER to Golgi to secretory vesicles and lysosomes, illustrating how membranes and proteins are trafficked within the cell.

Mitochondria and Ribosomes

  • Mitochondria:
    • Structure: Oblong organelles with double membrane; inner membrane folds form cristae; matrix inside the inner membrane.
    • Function: Produce ATP via aerobic cellular respiration; powerhouse of the cell.
    • Ribosomes: Mitochondria have their own ribosomes; also, ribosomes can be free in cytosol or attached to Rough ER.
  • Ribosomes:
    • Non-membrane-bound organelles composed of RNA and proteins.
    • Large and small subunits assembled in the nucleolus and then exported to cytosol.
    • Function: Protein synthesis; can be bound to rough ER or free in cytosol.

Other Important Cell Structures

  • Cytoskeleton: Intracellular structural support and organization of organelles; participates in cell division and movement; components include microtubules, intermediate filaments, and microfilaments.
  • Centrosome: Organizes microtubules for cell division.
  • Proteasomes: Digest unwanted or misfolded proteins.
  • Inclusions: Clusters of one type of molecule (e.g., pigments).
  • Plasma membrane components to learn: Cholesterol, lipid bilayer, polar heads, fatty acid tails, integral and peripheral membrane proteins, membrane channels.
  • Cytosol: Fluid within the cytoplasm; location of many metabolic pathways (glycolysis, etc.).
  • Nucleolus: Site of ribosome synthesis within the nucleus.

Cell Junctions – Structure, Location, and Function

  • Cell junctions are located between adjacent cells and are composed of integral and peripheral proteins.
  • Major types:
    • Tight junctions
    • Anchoring junctions (Desmosomes, Adherens, Hemidesmosomes)
    • Gap junctions
  • Tight junctions:
    • Form strands/rows of transmembrane proteins that seal intercellular spaces.
    • Function: Keeps substances from moving between epithelial cells; common in digestive tract and urinary bladder.
  • Anchoring junctions:
    • Desmosomes: Protein complexes that bind neighboring cells; include intermediate filaments; provide mechanical strength; common between cardiac muscle cells.
    • Hemidesmosomes: Anchor basal cell surface to underlying extracellular matrix (basement membrane).
    • Adherens: Similar to desmosomes but include actin; can pull edges together and assist tissue shape changes.
  • Gap junctions:
    • Composed of connexons (plasma proteins) that form intercellular channels.
    • Function: Allow passage of ions and small molecules; enable rapid spread of electrical activity in heart.
  • Key structural features: Cadherins (cell adhesion molecules in desmosomes and adherens), integrins (link to basal lamina), basement membrane, connexins in gap junctions.

Transcription and Translation – Protein Synthesis

  • Protein synthesis involves two main processes:
    • Transcription: Occurs in the nucleus; transcribes DNA into an RNA message.
    • DNA is confined to the nucleus; thus transcription enables reading information onto RNA to exit the nucleus.
    • Translation: Occurs in the cytoplasm at a ribosome; mRNA moves through a ribosome and the message is translated into a specific sequence of amino acids to form a protein.
  • Key concept: Gene vs chromosome
    • Gene: Functional unit of DNA that directs synthesis of a specific protein.
    • Chromosome: Structure that contains DNA packaged with proteins; genes are located on chromosomes.

Protein Synthesis – Steps and Visuals

  • Figure 4.35 outlines the steps:
    • In the nucleus: Transcription occurs; RNA polymerase synthesizes pre-mRNA using DNA template.
    • Pre-mRNA processing: Splicing and modification to form mature mRNA that exits the nucleus.
    • In the cytosol: Translation occurs at ribosomes; tRNA brings amino acids to form a polypeptide chain guided by mRNA codons.
    • mRNA, tRNA, ribosome interactions coordinate assembly of the protein.

The Cell Cycle, DNA Replication, and Mitosis

  • The cell cycle includes all stages from one cell division to the formation of two identical daughter cells.
  • Major phases:
    • Interphase: Cell grows, produces new organelles, and duplicates DNA; includes G1, S, and G2 phases.
    • Mitotic phase (M phase): Mitosis (nuclear division) and cytokinesis (cytoplasm division).
  • Interphase durations (from Fig. 4.40): ~23 hours total; G1 phase, S phase (DNA replication), G2 phase (growth and preparation), followed by M phase (~1 hour).
  • DNA, genes, and chromosomes:
    • DNA strands associated with histones form chromatin.
    • Chromatin condenses into chromosomes during mitosis.
    • The functional unit of DNA is a gene (a sequence directing protein synthesis).
  • DNA replication (Fig. 4.41): Four basic steps
    1) Unwinding of the DNA molecule
    2) Breaking hydrogen bonds between base pairs to separate parent strands
    3) Assembly of new DNA strands by DNA polymerase
    4) Restoration of the DNA double helix
  • Mitosis phases (Fig. 4.41):
    • Prophase: Chromatin condenses into chromosomes (composed of two sister chromatids); nucleolus breaks down; spindle fibers form; centrioles move to opposite poles; nuclear envelope breaks down.
    • Metaphase: Chromosomes align at the equatorial plate; spindle fibers attach to centromeres.
    • Anaphase: Sister chromatids separate and move toward opposite poles; centromeres split.
    • Telophase: Chromosomes arrive at poles and de-condense; nucleolus re-forms; spindle fibers disappear; new nuclear envelope forms around each set.
    • Cytokinesis: Division of cytoplasm; overlaps with anaphase/telophase; creates two distinct daughter cells.
  • Figure 4.42 summarizes interphase, mitosis, and cytokinesis with coordinated changes in chromosomes, spindle apparatus, and cell membrane.

Mitosis vs Meiosis – Roles in Humans

  • Mitosis:
    • Purpose: Divide a cell into two genetically identical diploid daughter cells.
    • Occurs in somatic (body) cells.
  • Meiosis:
    • Purpose: Reductive division to produce four haploid gametes (sperm or oocytes); two-step division with genetic variation.
    • Occurs in sex cells; essential for sexual reproduction.

Quick Reference – Key Equations and Timings

  • Interphase duration: ext{Interphase} \,\approx\, 23\ \text{hours}
  • M phase duration: M\text{ phase} \,\approx\, 1\ \text{hour}
  • ATP hydrolysis for primary active transport (e.g., Ca^{2+} pump): ATP + H2O → ADP + Pi; pump uses energy to move Ca^{2+} against its gradient.
  • Transport mechanisms (summary):
    • Diffusion, simple diffusion, facilitated diffusion (channel-mediated or carrier-mediated), osmosis
    • Primary and secondary active transport
    • Vesicular transport: exocytosis and endocytosis (phagocytosis, pinocytosis, receptor-mediated endocytosis)
    • Endocytosis components: clathrin-coated pits, receptor-ligand complexes

Connections and Real-World Relevance

  • The plasma membrane’s selective permeability underpins nutrient uptake, nerve impulse transmission, and muscle contraction via ion gradients.
  • Membrane transport mechanisms explain how neurons propagate signals (ion channel dynamics) and how kidneys regulate body fluids through osmosis and diffusion.
  • The endomembrane system coordinates protein processing for secretion (hormones, antibodies), lysosomal enzymes, and membrane synthesis—central to cellular function and health.
  • Cellular division is foundational for growth, tissue repair, and reproduction; errors in mitosis/meiosis can lead to cancer or genetic disorders.

Ethical, Philosophical, and Practical Implications

  • Understanding cell biology informs medical advances (cancer therapies targeting mitosis, genetic diseases, antiviral strategies) and ethical considerations around gene editing and reproductive technologies.
  • The study of cellular transport and membrane dynamics underpins drug delivery design and toxicity assessments (e.g., drug detoxification in the liver via SER and peroxisomes).

Quick Glossary (Key Terms)

  • Cytosol: Fluid inside the cell, excluding organelles.
  • Cytoplasm: Cytosol plus organelles, excluding nucleus.
  • Nucleolus: Site of ribosomal RNA synthesis and ribosome assembly.
  • Endomembrane system: Network of membranes including ER, Golgi, lysosomes, and vesicles involved in protein and lipid processing.
  • Glycocalyx: Carbohydrate-rich region on the cell surface involved in recognition and protection.
  • Cadherins, Integrins: Adhesion proteins involved in anchoring junctions.
  • Connexons: Protein assemblies forming gap junction channels.
  • Chromatids, Centromere: Structural components of condensed chromosomes during mitosis.
  • Centrosome: Microtubule organizing center important for spindle formation.
  • Proteasome: Protein-degrading complex.
  • Isotonic, Hypotonic, Hypertonic: Terms describing solution tonicity relative to cell cytosol.